Ankur Dhingra
Chief Financial Officer at Illumina
Thank you, Jacob and hello, everyone. I will be discussing non-GAAP results, which includes stock-based compensation. I encourage you to review the GAAP reconciliation of these non-GAAP measures, as well as our consolidated financials that include GRAIL, which can be found in today's release and in the supplementary data available on our website. In the last three months, I've had a chance to spend time with Illumina teams across all functions. I continue to be impressed with how mission-driven this team is and also how transformation is taking hold at Illumina. I've also heard from several of our investors as part of a listening tour. As I focus my commentary on the financial results and current outlook, I will include some additional color in my remarks.
Core Illumina second quarter revenue of $1.1 billion was down 6% year-over-year on both reported and constant currency basis and up 3% from the first quarter of 2024. These results exceeded our guidance. This above-expectations performance was driven primarily by continued increase in high-throughput sequencing consumables revenue as our customers further ramp activity on NovaSeq X Plus. This strength in consumables was partially offset by fewer-than-expected shipments of our mid-throughput instruments, as capital and cash flow constraints continue to impact our customers' purchasing decisions.
Total Core Illumina sequencing consumables revenue of $737 million was flat against last year's second quarter, which was the highest sequencing consumables revenue quarter of the year 2023. High throughput was a particularly bright spot in this year's second quarter, with consumable shipments growing both year-over-year and sequentially. Ex-consumables revenue grew 35% from the first quarter of 2024, accelerating from the double-digit sequential growth we saw in the first quarter. In order to provide some additional color on transition, as of Q2, approximately 45% of high-throughput giga bases sequenced and a little over 25% of high throughput consumables revenue, was on NovaSeq X Plus.
In terms of pace of shifting mix from 6000 to X, to date on average, roughly 5 percentage points of high throughput sequencing consumables revenue has moved from NovaSeq 6000 to NovaSeq X PLUS each quarter. As this transition progresses, the impact of price continues to reduce. If this trajectory holds, almost half of high throughput sequencing consumables revenue should transition to the NovaSeq X by mid-2025, continuing to reduce the impact of pricing transition and converting volume growth into higher revenue growth thereafter. I hope you find this additional information helpful. We are increasing our disclosures around the NovaSeq X to give you a clearer picture of the progress we are making in this important transition.
Moving to sequencing activity. total sequencing Gb output on our connected high and mid-throughput instruments grew more than 40% year-over-year and approximately 10% quarter-over-quarter. Growth in activity from both research and applied and clinical customers was healthy. Although not a predictor of near-term revenue, Gb output provides us a directional view of underlying applications demand and levels of utilization of our instruments and consumables. Sequencing instruments revenue for Core Illumina of $116 million for Q2 grew 5% sequentially but declined 40% year-over-year.
The year-over-year decline was driven by two factors: one, lower NovaSeq X placements as compared to significant preorder launch-related shipments in the second quarter of 2023; and two, an expected decline in mid-throughput shipments as capital and cash flow constraints continue to impact purchasing behavior and moderate instrument placements. Core Illumina sequencing service and other revenue of $143 million was up 7% year-over-year, driven by an increase in revenue from strategic partnerships as well, as higher instrument service contract revenue on a growing installed base.
Moving to the rest of the Core Illumina P&L. Core Illumina non-GAAP gross margins of 69.4% for the quarter increased 240 basis points year-over-year. This strong gross margin performance was driven primarily by a more favorable revenue mix of sequencing consumables and also, importantly, execution of our operational excellence initiatives that improved productivity and delivered cost savings. Core Illumina non-GAAP operating expenses of $516 million were down $15 million year-over-year, reflecting reductions in head count and several other cost containment initiatives. Putting it all together, Core Illumina non-GAAP operating margin was 22.2% in Q2 2024 compared to 21.2% in the prior year period. This came in well above our guidance of 18% as well as our expectations due to higher-than-expected revenue, better-than-expected gross margin and strides our organization has made in reducing operating expenses.
Below the operating income line, Core Illumina non-GAAP other expense of $13 million in Q2 includes 11 days of interest expense for the $750 million delayed draw term loan we drew in full on June 20, 2024. Core Illumina non-GAAP net income for Q2 was $174 million or $1.09 per diluted share. Core Illumina non-GAAP tax rate was 24.2% for the quarter. Our non-GAAP weighted average diluted share count for the quarter was approximately 159 million. Moving to Core Illumina cash flow and balance sheet items for the quarter. Cash flow provided by operations was $243 million. Capex were $30 million and free cash flow was $213 million. We ended the quarter with approximately $994 million in cash, cash equivalents and short-term investments.
Moving now to 2024 guidance. While we were encouraged by our results in Q2, we see several puts and takes as we consider the remainder of the year. On one hand, our customers' capital spending remains constrained. On the other hand, our Consumables business, especially high-throughput, driven by the transition of NovaSeq X, remains solid. We are therefore reducing our revenue expectations, especially for Instruments, for the second half of the year. Core Illumina full year revenue is now projected to be down 2% to 3% from 2023 or down 1.5% to 2.5% on a constant currency basis. Approximately one-half of the decline from our prior guidance is due to our lower expectations for our business in China and broader Asia. And the other half is a result of our reduced expectations for mid-throughput and NovaSeq X shipments.
From an instruments versus consumables perspective, at the midpoint of the Core Illumina revenue guidance range, sequencing instruments revenue is now projected to decline in the mid-30s rate, relative to 2023. Sequencing consumables revenue is now projected to grow towards the upper end of the low single-digit range versus 2023. Now about the remainder of P&L. Illumina has been able to execute on stated operational excellence initiatives, delivering operating leverage above our previous expectations. We thus are raising our Core Illumina non-GAAP operating margin guidance to a range of 20.5% to 21%. This reflects the margin expansion achieved in Q2 2024, but we are also reducing our forecasted operating expenses for the second half of the year.
We continue to make progress against our expense actions as well as several operational excellence initiatives under our internal Pinnacle Continuous Improvement Program. We've now launched several new initiatives under this Continuous Improvement Program, which we expect will deliver an additional $200 million in expense savings over the next few years. We'll talk about this in more detail at the upcoming strategy update. Additionally, we expect the Core Illumina non-GAAP tax rate to be approximately 25%.
And lastly, we are introducing guidance for Core Illumina non-GAAP diluted earnings per share in the range of $3.80 and $3.95 for full year 2024. This range includes second half interest expense resulting from the $750 million delayed draw term loan we put in place in June this year. For the third quarter of 2024, we expect Core Illumina revenue in the range of $1.075 billion to $1.085 billion. The decline from the prior year is driven predominantly by lower NovaSeq X instrument shipments given the significant backlog we worked through last year following the launch.
For the third quarter, we also expect Core Illumina non-GAAP operating margin of approximately 20%. The sequential decrease from the second quarter is primarily due to lower revenue and timing of the project spend delayed from Q2. We expect the third quarter non-GAAP Core Illumina tax rate to be approximately 25% and Core Illumina non-GAAP diluted EPS between $0.80 and $0.90 which, again, includes the said interest expense.
With that, I will now turn it back over to Jacob for his closing remarks. Thank you.